Experimental conditions obtained on the DIII-D tokamak in the ITER Similar Shape (ISS) have been compared extensively with nonlinear gyrokinetic simulation using the CGYRO code [Candy et al., J. Comput. Phys. 324, 73–93 (2016)] with comparisons spanning ion and electron heat fluxes, electron and impurity particle transport, and turbulent fluctuation levels and characteristics. Bayesian optimization techniques [Rodriguez-Fernandez et al., Nucl. Fusion 62(7), 076036 (2022)], combined with nonlinear gyrokinetics, have been used to obtain simultaneously Qi, Qe, and Γe flux-matched profiles that are found to be in good agreement with experimental profile measurements. Synthetic diagnostics were used to compare measured beam emission spectroscopy and correlation electron cyclotron emission turbulent fluctuations with nonlinear simulation. Although some disagreements exist, nonlinear simulations are found to be in generally good agreement with measured fluctuation levels, spectral shapes, and measured radial trends in low-k δne/ne and δTe/Te. Low (Li and C) and mid-Z (Ca) impurity transport was also compared with these flux-matched simulations. Fully stripped, low-Z impurities are well reproduced by the gyrokinetic modeling while clear disagreement exists in comparisons with mid-Z impurities. Nonlinear gyrokinetic investigation into the Z dependence of impurity transport in the ISS conditions is also performed, demonstrating clear trends of impurity diffusion with impurity Z (both D∝Z and D∝1/Z) that vary with the radial location studied. These trends are shown to result from the local dominance of ion temperature gradient or ∇n driven trapped electron mode turbulence and may contribute to the disagreement between simulation and experiment in mid-Z impurity transport. The results of this work represent one of the most complete validation studies of the gyrokinetic model performed to date and provide an example of new capabilities for predicting performance in future fusion devices.